[2024-01-24 11:05:25,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference
[2024-01-24 11:05:26,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,773] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fba1f46-f597-472f-b724-d5ba9a0de335/GCF_002355535.1_ASM235553v1_genomic.fna.gz | prodigal -d GCF_002355535.1_ASM235553v1_genomic.fna/cds.fna -a GCF_002355535.1_ASM235553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:31,790] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:31,791] [INFO] Task started: HMMsearch
[2024-01-24 11:05:31,791] [INFO] Running command: hmmsearch --tblout GCF_002355535.1_ASM235553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/reference_markers.hmm GCF_002355535.1_ASM235553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:32,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:32,030] [INFO] Found 6/6 markers.
[2024-01-24 11:05:32,052] [INFO] Query marker FASTA was written to GCF_002355535.1_ASM235553v1_genomic.fna/markers.fasta
[2024-01-24 11:05:32,052] [INFO] Task started: Blastn
[2024-01-24 11:05:32,052] [INFO] Running command: blastn -query GCF_002355535.1_ASM235553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/reference_markers.fasta -out GCF_002355535.1_ASM235553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:32,720] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:32,724] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:32,725] [INFO] Target genome list was writen to GCF_002355535.1_ASM235553v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:32,746] [INFO] Task started: fastANI
[2024-01-24 11:05:32,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fba1f46-f597-472f-b724-d5ba9a0de335/GCF_002355535.1_ASM235553v1_genomic.fna.gz --refList GCF_002355535.1_ASM235553v1_genomic.fna/target_genomes.txt --output GCF_002355535.1_ASM235553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:44,691] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:44,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:44,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:44,705] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:44,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:44,706] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Aurantimicrobium minutum	strain=KNC	GCA_002355535.1	708131	708131	type	True	100.0	540	540	95	conclusive
Aurantimicrobium photophilum	strain=MWH-Mo1	GCA_003194085.1	1987356	1987356	type	True	82.3796	329	540	95	below_threshold
Alpinimonas psychrophila	strain=DSM 23737	GCA_014137865.1	748908	748908	type	True	78.7568	88	540	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	78.4808	50	540	95	below_threshold
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	77.9547	65	540	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	77.7244	63	540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:44,708] [INFO] DFAST Taxonomy check result was written to GCF_002355535.1_ASM235553v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:44,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:44,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:44,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/checkm_data
[2024-01-24 11:05:44,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:44,734] [INFO] Task started: CheckM
[2024-01-24 11:05:44,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355535.1_ASM235553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355535.1_ASM235553v1_genomic.fna/checkm_input GCF_002355535.1_ASM235553v1_genomic.fna/checkm_result
[2024-01-24 11:06:06,526] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:06,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,546] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:06,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:06,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355535.1_ASM235553v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:06,548] [INFO] Task started: Blastn
[2024-01-24 11:06:06,548] [INFO] Running command: blastn -query GCF_002355535.1_ASM235553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg276d2616-9bf7-4c1d-83bb-04e086204be0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355535.1_ASM235553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:07,584] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:07,587] [INFO] Selected 13 target genomes.
[2024-01-24 11:06:07,587] [INFO] Target genome list was writen to GCF_002355535.1_ASM235553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:07,598] [INFO] Task started: fastANI
[2024-01-24 11:06:07,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fba1f46-f597-472f-b724-d5ba9a0de335/GCF_002355535.1_ASM235553v1_genomic.fna.gz --refList GCF_002355535.1_ASM235553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355535.1_ASM235553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:13,358] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,367] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:13,367] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002355535.1	s__Aurantimicrobium minutum	100.0	540	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003325955.1	s__Aurantimicrobium sp003325955	90.5637	484	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194085.1	s__Aurantimicrobium sp003194085	82.3796	329	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137865.1	s__Alpinimonas psychrophila	78.7568	88	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Alpinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859205.1	s__CAIOLM01 sp903859205	78.6652	83	540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__CAIOLM01	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,369] [INFO] GTDB search result was written to GCF_002355535.1_ASM235553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:13,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:13,372] [INFO] DFAST_QC result json was written to GCF_002355535.1_ASM235553v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:13,373] [INFO] DFAST_QC completed!
[2024-01-24 11:06:13,373] [INFO] Total running time: 0h0m48s